# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 21:56:08 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[(2~{R})-2,3-bis(oxidanyl)propyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC[C@H](O)CO)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 P9S  P9S  '(2~{R})-2-azanyl-3-[(2~{R})-2,3-bis(oxidanyl)propyl]sulfanyl-propanoic acid'  L-peptide  24  12  .  2019-03-22  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P9S
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 P9S  OAK  O  OH1    0  -0.667   3.5626  -21.0164  -24.6583
 P9S  CAI  C  CH2    0  -0.174   2.2237  -21.1877  -24.2553
 P9S  CAH  C  CH1    0   0.014   1.3602  -21.3492  -25.5019
 P9S  OAJ  O  OH1    0  -0.664   0.0158  -21.5821  -25.1450
 P9S  CAG  C  CH2    0  -0.557   1.3875  -20.1395  -26.4208
 P9S  SAF  S  S2     0  -0.048   0.5980  -18.6917  -25.6468
 P9S  CB   C  CH2    0  -0.551   1.3674  -17.3583  -26.6071
 P9S  CA   C  CH1    0  -0.181   0.6663  -17.0887  -27.9275
 P9S  N    N  NH2    0  -0.811   1.5086  -16.2051  -28.7339
 P9S  C    C  C      0   0.419  -0.7140  -16.4001  -27.7633
 P9S  O    O  O      0  -0.590  -1.0842  -16.0850  -26.6186
 P9S  H1   H  HOH1   0   0.455   4.1011  -20.8964  -23.8715
 P9S  H2   H  HCH2   0   0.196   1.8585  -20.3381  -23.6659
 P9S  H3   H  HCH2   0   0.201   2.1042  -22.0879  -23.6348
 P9S  H4   H  HCH1   0   0.220   1.7644  -22.1932  -26.0813
 P9S  H5   H  HOH1   0   0.451  -0.0309  -22.3952  -24.6313
 P9S  H6   H  HCH2   0   0.264   2.4219  -19.8924  -26.6612
 P9S  H7   H  HCH2   0   0.266   0.8816  -20.3821  -27.3573
 P9S  H8   H  HCH2   0   0.251   2.4150  -17.6277  -26.7668
 P9S  H9   H  HCH2   0   0.258   1.3523  -16.4675  -25.9797
 P9S  H10  H  HCH1   0   0.196   0.4932  -18.0573  -28.4258
 P9S  H11  H  HNH2   0   0.335   2.3222  -16.7147  -29.0568
 P9S  H12  H  HNH2   0   0.334   0.9931  -15.9470  -29.5661
 P9S  O1   O  OC    -1  -0.617  -1.3306  -16.2050  -28.8317

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 P9S  N    CA   single  1.458  0.019  1.458
 P9S  CA   C    single  1.525  0.021  1.525
 P9S  CA   CB   single  1.530  0.020  1.530
 P9S  C    O    deloc   1.231  0.020  1.231
 P9S  CAG  CAH  single  1.519  0.020  1.519
 P9S  CAG  SAF  single  1.822  0.020  1.822
 P9S  CB   SAF  single  1.815  0.020  1.815
 P9S  OAJ  CAH  single  1.410  0.020  1.410
 P9S  CAH  CAI  single  1.525  0.020  1.525
 P9S  OAK  CAI  single  1.409  0.020  1.409
 P9S  OAK  H1   single  0.850  0.020  0.980
 P9S  CAI  H2   single  0.970  0.020  1.090
 P9S  CAI  H3   single  0.970  0.020  1.090
 P9S  CAH  H4   single  0.970  0.020  1.090
 P9S  OAJ  H5   single  0.850  0.020  0.980
 P9S  CAG  H6   single  0.970  0.020  1.090
 P9S  CAG  H7   single  0.970  0.020  1.090
 P9S  CB   H8   single  0.970  0.020  1.090
 P9S  CB   H9   single  0.970  0.020  1.090
 P9S  CA   H10  single  0.970  0.020  1.090
 P9S  N    H11  single  0.890  0.020  1.040
 P9S  N    H12  single  0.890  0.020  1.040
 P9S  C    O1   deloc   1.249  0.020  1.249

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 P9S  H1   OAK  CAI  108.27  3.000
 P9S  H3   CAI  H2   107.14  3.000
 P9S  H3   CAI  CAH  108.24  3.000
 P9S  H2   CAI  CAH  109.44  3.000
 P9S  H3   CAI  OAK  111.36  3.000
 P9S  H2   CAI  OAK  112.09  3.000
 P9S  CAH  CAI  OAK  108.49  3.000
 P9S  H4   CAH  CAG  106.59  3.000
 P9S  H4   CAH  OAJ  110.89  3.000
 P9S  CAG  CAH  OAJ  107.56  3.000
 P9S  H4   CAH  CAI  107.67  3.000
 P9S  OAJ  CAH  CAI  110.51  3.000
 P9S  CAG  CAH  CAI  113.57  3.000
 P9S  H5   OAJ  CAH  108.70  3.000
 P9S  H7   CAG  H6   107.51  3.000
 P9S  H7   CAG  SAF  109.90  3.000
 P9S  H6   CAG  SAF  108.95  3.000
 P9S  H7   CAG  CAH  109.48  3.000
 P9S  H6   CAG  CAH  109.32  3.000
 P9S  SAF  CAG  CAH  111.59  3.000
 P9S  CB   SAF  CAG  100.10  3.000
 P9S  H9   CB   H8   107.39  3.000
 P9S  H9   CB   CA   110.43  3.000
 P9S  H8   CB   CA   111.04  3.000
 P9S  H9   CB   SAF  106.87  3.000
 P9S  H8   CB   SAF  107.61  3.000
 P9S  CA   CB   SAF  113.25  3.000
 P9S  H10  CA   C    107.34  3.000
 P9S  H10  CA   N    111.82  3.000
 P9S  C    CA   N    111.00  2.800
 P9S  H10  CA   CB   108.02  3.000
 P9S  C    CA   CB   110.10  1.900
 P9S  N    CA   CB   110.50  1.700
 P9S  H12  N    H11  105.97  3.000
 P9S  H12  N    CA   108.30  3.000
 P9S  H11  N    CA   109.53  3.000
 P9S  O1   C    O    126.93  3.000
 P9S  O1   C    CA   114.72  3.000
 P9S  O    C    CA   120.80  1.700

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 P9S  Var_01  CA  CB   SAF  CAG  83.81  30.0  1
 P9S  Var_02  H6  CAG  SAF  CB   37.12  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 P9S  chir_01  CAH  CAG  OAJ  CAI  positiv
 P9S  chir_02  CA   N    C    CB   positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 P9S  plan-1  CA  0.020
 P9S  plan-1  C   0.020
 P9S  plan-1  O   0.020
 P9S  plan-1  O1  0.020

